ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtgagctttgttgaaattttgttgtgtaggatgtttgttgggtagatgtttttcattattctgtgtccctgttcgacgattgtgtgtttctccatgtctgattcggtcctctcatacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG

Basic information

species	Physcomitrella patens
transcript	PP1S8_312V6.1
intron #	17
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 16

gtgagctttgttgaaattttgttgtgtaggatgtttgttgggtagatgtttttcattattctgtgtccctgttcgacgattgtgtgtttctccatgtctgattcggtcctctcatacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG
|||||   |     | |||| |            |  ||   || |  ||| |   |  ||| | |     ||  | ||||     |||      ||||||| |    || |   | |  |||| |||||||| ||||| ||||||||||||||||| ||||||||||| || ||| | || ||||| ||  | |||||||||
gtgagtcataccctagttttttc-----------tgatttaatacagatttattggttgtctctat-----tttaatgattaaccattttctttagtctgat-catctctatataatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAG

upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 16

gtgagctttgttgaaattttgttgtgtaggatgtttgttgggtagatgtttttcattattctgtgtccctgttcgacgattgtgtgtttctccatgtctgattcggtcctctcatacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG---------------------
|||||   |     | |||| |            |  ||   || |  ||| |   |  ||| | |     ||  | ||||     |||      ||||||| |    || |   | |  |||| |||||||| ||||| ||||||||||||||||| ||||||||||| || ||| | || ||||| ||  | |||||||||                     
gtgagtcataccctagttttttc-----------tgatttaatacagatttattggttgtctctat-----tttaatgattaaccattttctttagtctgat-catctctatataatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGGTAAATCTAACGTGTTTTTAC

upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 16

gtgagctttgttgaaattttgttgtgtaggatgtttgttgggtagatgtttttcattattctgtgtccctgttcgacgattgtgtgtttctccatgtctgattcggtcctctcatacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG
                                   ||   | || |    ||| ||  ||||     |||||   |  ||    | ||     ||   |||| |  | || |   | |  |||| ||||| || |  |||||||||||||| ||||| ||||||||||| || ||| | || ||||||||  | ||||  |||
----------------------------------gtgagtgttaaacccatttgatagttctactaacctgtgtcataatc-catattaactaat---tgat-caattctgttgcatgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG

upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 13

gtgagctttgttgaaattttgttgtgtaggatgtttgttgggtagatgtttttcattattctgtgtccctgttcgacgattgtgtgtttctccatgtctgattcggtcctctcatacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG
                      |   |||        |   |    ||  | | |  ||| | |   | | ||   | ||| | | |||       |        ||  | |   |  |   || ||||| || ||||||||||||||||| || || ||||||||||| |||||| | |||||||||||  | |||||||||
---------------------atac-tagaccaaaaatcaagattttgggtgttacaattttctactcatatttctccattttattttttaaataattctgacaagtgttgtttaatat--tagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG

upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 16

gtgagctttgttgaaattttgttgtgtaggatgtttgttgggtagatgtttttcattattctgtgtccctgttcgacgattgtgtgtttctccatgtctgattcggtcctctcatacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG
                                ||  ||    ||  | |||      |||   ||  | | ||   | ||| | | ||      | | |      || || |   |    | || ||||| || ||||||||||||||||| || || ||||||||||| || ||| | |||||||||||  | |||||||||
--------------------------------gtgagtcccctacttatttcaacacatttgatgctcatttttctccattatattttaagtatttttttgacaagtgctgtttaattatatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACATTATTCACTTCAACACATTGGCAAATCAG

upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 17

gtgagctttgttgaaattttgttgtgtaggatgtt-tgttgggtagatgtttttcat-tattctgtgtccctgttcgacgattgtgtgtttctccatgtctgattcggtcctctcatacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG
                       ||   |||  || |  | |||  |  | ||| || | |  | | |   ||||      || | ||||  |  ||||  |   |  |          |||| || ||||||||||||||||| |||||||||||||| ||||||||||| || ||| |||| ||| ||| | | |||||||||
-----------------------gtaagggaccttgtaattggttaacttctttaatatgtattatattattgttt-----ttatttgttctt--atgttggtacctttttgtgtggctgtgatagATATGACAAATTCTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAG

upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 17

gtgagctttgttgaaattttgttgtgtaggatgtttgttgggtagatgtttttcattattctgtgtccctgttcgacgattgtgtgtttctccatgtctgattcggtcctctcatacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG
                         ||| |     |  |   | | |   ||   | |   |       | ||  |  |||||||  ||    |||| || | |  ||         |||| || ||||| ||||| ||||| |||||||||||||| ||||||||||| || ||| |||| ||| ||| | | |||||||||
-------------------------gtaagggcccttgtaattggttaacttctttaacatt-------tattatattattgtgttctt----atgt-tggtaccttctgtgtggctgtgatagATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAG

upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 17

gtgagctttgttgaaattttgttgtgtaggatgtttgttgggtagatgtttttcattattctgtgtccctgttcgacgattgtgtgtttctccatgtctgattcggtcctctca--tacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG
                         ||| |||  ||||||| |   |   |||   | |  |   || || ||   |  |     | || | ||    |||  |  |    | |  |   |||||| |||||||||||||| || ||||||||||| ||||||||||||||||| ||| |||| ||| |||  || || || |||
-------------------------gtaagat--ttgttggctcccttcgttttggtttagtac-tctctctttctctctcaacgggttattcactcttgaaccttttggatgaattttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG

upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 17

------------gtgagcttt--gttgaaatttt-gttgtgtaggatgtttgttgggtagatgtttt-tcattattctgtgtccctgttcgacgattgtgtgtttctccatgtctgattcggtcctctcata--cgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG
             | || |||   || ||||||| ||  | |   || ||||||   |   | |||  | ||  | |  | |   || | | | |     | ||| ||||  |   ||  |   |||   |    ||||||| ||||| || |||||||| ||||||||||| || ||||||||||| |||||| |||| ||| | | | | || ||||||
gtaagtcccagattaagtttttgattcaaattttcgtcctttttaatttttgtttacttactatttccttatgttcccctttttatgctggtctagaaattctttttccacttaatatatgtatctcatgtggctgtgacagATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|162149954|gb|FC326277.1|FC326277

EST:     GTTGCTAAACTCTTGAGAGAGGACTATTTGGCGCAGAATGCTTTTAGCAG                         TTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATAT
genomic: GTTGCTAAACTCTTGAGAGAGGACTATTTGGCGCAGAATGCTTTTAGCAGgtgagctttg ... tacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATAT

EST: gi|162154256|gb|FC330387.1|FC330387

EST:     GTTGCTAAACTCTTGAGAGAGGACTATTTGGCGCAGAATGCTTTTAGCAG                         TTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATAT
genomic: GTTGCTAAACTCTTGAGAGAGGACTATTTGGCGCAGAATGCTTTTAGCAGgtgagctttg ... tacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATAT

EST: gi|208354120|gb|DC957382.1|DC957382

EST:     GTTGCTAAACTCTTGAGAGAGGACTATTTGGCGCAGAATGCTTTTAGCAG                         TTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATAT
genomic: GTTGCTAAACTCTTGAGAGAGGACTATTTGGCGCAGAATGCTTTTAGCAGgtgagctttg ... tacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATAT

EST: gi|37843692|gb|BJ601700.1|BJ601700

EST:     GTTGCTAAACTCTTGAGAGAGGACTATTTGGCGCAGAATGCTTTTAGCAG                         TTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATAT
genomic: GTTGCTAAACTCTTGAGAGAGGACTATTTGGCGCAGAATGCTTTTAGCAGgtgagctttg ... tacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATAT

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 1 RNA-Seqlibrary.

Block sizes: 13 (upstream exon), 28 (downstream exon)
Score: 2

CTTGTTGGAAAGGATGCTTTGGCAGAAACTGATAAAATCACCTTGGAAGTTGCTAAACTCTTGAGAGAGGACTATTTGGCGCAGAATGCTTTTAGCAGgtgagctttg ... tacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgttcgacgattgtgtgtttctccatgtctgattcggtcctctcatacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG